Commit 676c7e7e authored by samuel hanot's avatar samuel hanot
Browse files

update get_maps to use curl instead of links to get cutoff

parent bd8eaaea
#!/bin/bash #!/bin/bash
bindir=$(dirname $0) bindir=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
rec_gmconvert=${bindir}/recursive_gmconvert.sh
echo "rec_gmconvert=${rec_gmconvert}"
source ${bindir}/modules.sh source ${bindir}/modules.sh
for f in $(cat) for f in $(cat)
...@@ -10,12 +11,12 @@ do ...@@ -10,12 +11,12 @@ do
echo $f echo $f
rsync -a -v -z --delete rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-${f}/ $f rsync -a -v -z --delete rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-${f}/ $f
cd $f cd $f
links http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-$f/analysis > header/map_analysis.txt curl http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-$f/analysis > header/map_analysis.html
cutoff=$(awk '/contour/{print $4}' < header/map_analysis.txt) cutoff=$(awk '/contour/{print 3}' < header/map_analysis.html)
resolution=$(sed -ne 's/[<>/ ]//g' -ne 's/resolutionByAuthor//gp' header/emd-${f}.xml) resolution=$(sed -ne 's/[<>/ ]//g' -ne 's/resolutionByAuthor//gp' header/emd-${f}.xml)
echo ${cutoff} > cutoff.txt echo ${cutoff} > cutoff.txt
echo ${resolution} > resolution.txt echo ${resolution} > resolution.txt
gunzip -c map/emd_${f}.map.gz > emd_${f}.map gunzip -c map/emd_${f}.map.gz > emd_${f}.map
${bindir}/recursive_gmconvert.sh emd_${f}.map $cutoff $1 $2 ${rec_gmconvert} -f emd_${f}.map -t $cutoff -n $1 -N $2
cd - cd -
done done
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